Stderr output

<core_client_version>7.14.2</core_client_version>
<![CDATA[
<stderr_txt>
05:05:32 (3109): wrapper (7.7.26015): starting
05:05:32 (3109): wrapper: running run_atlas (--nthreads 1)
2019-08-19 05:05:32,878: singularity image is /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6
2019-08-19 05:05:32,878: sys.argv = ['run_atlas', '--nthreads', '1']
2019-08-19 05:05:32,881: THREADS=1

2019-08-19 05:05:32,883: Checking for CVMFS
2019-08-19 05:05:49,658: CVMFS is installed
2019-08-19 05:05:49,665: OS:CentOS Linux release 7.4.1708 (Core) 
2019-08-19 05:05:49,666: This is not SLC6, need to run with Singularity....
2019-08-19 05:05:49,666: Checking Singularity...
2019-08-19 05:05:49,691: Singularity is installed, version 2.6.1-dist
2019-08-19 05:05:49,691: Testing the function of Singularity...
2019-08-19 05:05:49,692: Checking singularity with cmd:singularity exec -B /cvmfs /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6 hostname
2019-08-19 05:05:52,622: Singularity Works...
2019-08-19 05:05:52,624: copy /root/slots/0/shared/ATLAS.root_0
2019-08-19 05:05:55,068: copy /root/slots/0/shared/input.tar.gz
2019-08-19 05:05:55,070: copy /root/slots/0/shared/RTE.tar.gz
2019-08-19 05:05:55,071: copy /root/slots/0/shared/start_atlas.sh
2019-08-19 05:05:55,157: start atlas job with PandaID=4451629869
2019-08-19 05:05:55,157: cmd = singularity exec --pwd /root/slots/0 -B /cvmfs,/root /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/x86_64-slc6 sh start_atlas.sh > runtime_log 2> runtime_log.err
2019-08-21 09:08:05,055: running cmd return value is 0
2019-08-21 09:08:05,057: Moving ./HITS.18722326._014041.pool.root.1 to shared/HITS.pool.root.1
2019-08-21 09:08:05,059: *****************The last 100 lines of the pilot log******************
2019-08-21 09:08:05,075: 2019-08-21 07:07:03,452 | DEBUG    | queue_monitor       | pilot.control.job                | send_state                | wrote heartbeat to file /root/slots/0/heartbeat.json
2019-08-21 07:07:03,452 | INFO     | queue_monitor       | pilot.control.job                | queue_monitor             | job 4451629869 was dequeued from the monitored payloads queue
2019-08-21 07:07:04,478 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-21 07:07:04,478 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | job summary report
2019-08-21 07:07:04,478 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-21 07:07:04,479 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | PanDA job id: 4451629869
2019-08-21 07:07:04,479 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | task id: 18722326
2019-08-21 07:07:04,479 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | errors: (none)
2019-08-21 07:07:04,479 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | status: LOG_TRANSFER = DONE 
2019-08-21 07:07:04,479 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pilot state: finished 
2019-08-21 07:07:04,480 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | transexitcode: 0
2019-08-21 07:07:04,480 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrorcode: 0
2019-08-21 07:07:04,480 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exeerrordiag: 
2019-08-21 07:07:04,480 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitcode: 0
2019-08-21 07:07:04,481 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | exitmsg: OK
2019-08-21 07:07:04,481 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | cpuconsumptiontime: 178158 s
2019-08-21 07:07:04,481 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | nevents: 200
2019-08-21 07:07:04,481 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | neventsw: 0
2019-08-21 07:07:04,481 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pid: 10159
2019-08-21 07:07:04,482 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | pgrp: 10159
2019-08-21 07:07:04,482 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | corecount: 1
2019-08-21 07:07:04,482 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | event service: False
2019-08-21 07:07:04,482 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | --------------------------------------------------
2019-08-21 07:07:04,482 | INFO     | retrieve            | pilot.util.auxiliary             | make_job_report           | 
2019-08-21 07:07:04,482 | INFO     | retrieve            | pilot.control.job                | has_job_completed         | job 4451629869 has completed
2019-08-21 07:07:04,483 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | overall cleanup function is called
2019-08-21 07:07:04,486 | DEBUG    | retrieve            | pilot.util.processes             | cleanup                   | work directory was removed: /root/slots/0/PanDA_Pilot-4451629869
2019-08-21 07:07:05,491 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | --- collectZombieJob: --- 10, [10159]
2019-08-21 07:07:05,491 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | zombie collector trying to kill pid 10159
2019-08-21 07:07:05,491 | INFO     | retrieve            | pilot.info.jobdata               | collect_zombies           | harmless exception when collecting zombies: [Errno 10] No child processes
2019-08-21 07:07:06,496 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | collected zombie processes
2019-08-21 07:07:06,497 | INFO     | retrieve            | pilot.util.processes             | cleanup                   | will now attempt to kill all subprocesses of pid=10159
2019-08-21 07:07:06,563 | INFO     | retrieve            | pilot.util.processes             | kill_processes            | process IDs to be killed: [10159] (in reverse order)
2019-08-21 07:07:06,657 | WARNING  | retrieve            | pilot.util.processes             | kill_processes            | found no corresponding commands to process id(s)
2019-08-21 07:07:06,657 | INFO     | retrieve            | pilot.util.processes             | kill_orphans              | Do not look for orphan processes in BOINC jobs
2019-08-21 07:07:06,658 | INFO     | retrieve            | pilot.control.job                | retrieve                  | ready for new job
2019-08-21 07:07:06,658 | INFO     | retrieve            | root                             | retrieve                  | pilot has finished for previous job - re-establishing logging
No handlers could be found for logger "pilot.util.mpi"
2019-08-21 07:07:07,165 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | getjob_requests=1
2019-08-21 07:07:17,213 | DEBUG    | retrieve            | pilot.control.job                | proceed_with_getjob       | proceed_with_getjob called with getjob_requests=1
2019-08-21 07:07:17,213 | DEBUG    | retrieve            | pilot.util.monitoring            | check_local_space         | checking local space on /root/slots/0
2019-08-21 07:07:17,260 | INFO     | retrieve            | pilot.util.monitoring            | check_local_space         | sufficient remaining disk space (7232028672 B)
2019-08-21 07:07:17,260 | WARNING  | retrieve            | pilot.control.job                | proceed_with_getjob       | since timefloor is set to 0, pilot was only allowed to run one job
2019-08-21 07:07:17,260 | DEBUG    | retrieve            | pilot.control.job                | retrieve                  | [job] retrieve thread has finished
2019-08-21 07:07:17,261 | WARNING  | queue_monitoring    | pilot.util.common                | should_abort              | data:queue_monitoring:received graceful stop - abort after this iteration
2019-08-21 07:07:17,261 | WARNING  | copytool_out        | pilot.util.common                | should_abort              | data:copytool_out:received graceful stop - abort after this iteration
2019-08-21 07:07:17,334 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 16 threads
2019-08-21 07:07:17,335 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140505133541120)>, <ExcThread(job, started 140504916436736)>, <ExcThread(validate_post, started 140504326981376)>, <ExcThread(job_monitor, started 140504788350720)>, <ExcThread(validate_pre, started 140504771565312)>, <ExcThread(monitor, started 140504352159488)>, <ExcThread(payload, started 140504796743424)>, <ExcThread(copytool_out, started 140504805136128)>, <ExcThread(queue_monitoring, started 140504779958016)>, <ExcThread(copytool_in, started 140504335374080)>, <ExcThread(queue_monitor, started 140504343766784)>, <ExcThread(failed_post, started 140504318588672)>, <ExcThread(execute_payloads, started 140504310195968)>, <ExcThread(create_data_payload, started 140504821921536)>, <ExcThread(data, started 140504899651328)>, <ExcThread(validate, started 140504908044032)>]
2019-08-21 07:07:17,364 | INFO     | validate_post       | pilot.control.payload            | validate_post             | [payload] validate_post thread has finished
2019-08-21 07:07:17,365 | INFO     | failed_post         | pilot.control.payload            | failed_post               | [payload] failed_post thread has finished
2019-08-21 07:07:17,443 | DEBUG    | copytool_in         | pilot.control.data               | copytool_in               | [data] copytool_in thread has finished
2019-08-21 07:07:17,444 | INFO     | execute_payloads    | pilot.control.payload            | execute_payloads          | [payload] execute_payloads thread has finished
2019-08-21 07:07:17,444 | INFO     | validate_pre        | pilot.control.payload            | validate_pre              | [payload] validate_pre thread has finished
2019-08-21 07:07:17,444 | DEBUG    | validate            | pilot.control.job                | validate                  | [job] validate thread has finished
2019-08-21 07:07:17,445 | DEBUG    | create_data_payload | pilot.control.job                | create_data_payload       | [job] create_data_payload thread has finished
2019-08-21 07:07:17,450 | INFO     | monitor             | pilot.control.monitor            | control                   | [monitor] control thread has ended
2019-08-21 07:07:17,493 | DEBUG    | payload             | pilot.control.payload            | control                   | payload control ending since graceful_stop has been set
2019-08-21 07:07:17,494 | DEBUG    | payload             | pilot.control.payload            | control                   | [payload] control thread has finished
2019-08-21 07:07:17,596 | DEBUG    | job                 | pilot.control.job                | control                   | job control ending since graceful_stop has been set
2019-08-21 07:07:17,596 | DEBUG    | job                 | pilot.control.job                | control                   | [job] control thread has finished
2019-08-21 07:07:17,638 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 6 threads
2019-08-21 07:07:17,638 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140505133541120)>, <ExcThread(job_monitor, started 140504788350720)>, <ExcThread(copytool_out, started 140504805136128)>, <ExcThread(queue_monitoring, started 140504779958016)>, <ExcThread(queue_monitor, started 140504343766784)>, <ExcThread(data, started 140504899651328)>]
2019-08-21 07:07:18,129 | DEBUG    | data                | pilot.control.data               | control                   | data control ending since graceful_stop has been set
2019-08-21 07:07:18,129 | DEBUG    | data                | pilot.control.data               | control                   | [data] control thread has finished
2019-08-21 07:07:18,142 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 5 threads
2019-08-21 07:07:18,142 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140505133541120)>, <ExcThread(job_monitor, started 140504788350720)>, <ExcThread(copytool_out, started 140504805136128)>, <ExcThread(queue_monitoring, started 140504779958016)>, <ExcThread(queue_monitor, started 140504343766784)>]
2019-08-21 07:07:18,262 | DEBUG    | copytool_out        | pilot.control.data               | copytool_out              | [data] copytool_out thread has finished
2019-08-21 07:07:18,344 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 4 threads
2019-08-21 07:07:18,344 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140505133541120)>, <ExcThread(job_monitor, started 140504788350720)>, <ExcThread(queue_monitoring, started 140504779958016)>, <ExcThread(queue_monitor, started 140504343766784)>]
2019-08-21 07:07:18,995 | WARNING  | queue_monitor       | pilot.util.common                | should_abort              | job:queue_monitor:received graceful stop - abort after this iteration
2019-08-21 07:07:18,996 | DEBUG    | queue_monitor       | pilot.control.job                | queue_monitor             | [job] queue monitor thread has finished
2019-08-21 07:07:19,049 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 3 threads
2019-08-21 07:07:19,049 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140505133541120)>, <ExcThread(job_monitor, started 140504788350720)>, <ExcThread(queue_monitoring, started 140504779958016)>]
2019-08-21 07:07:20,264 | DEBUG    | queue_monitoring    | pilot.control.data               | queue_monitoring          | [data] queue_monitor thread has finished
2019-08-21 07:07:20,357 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | thread count now at 2 threads
2019-08-21 07:07:20,358 | DEBUG    | MainThread          | pilot.workflow.generic           | run                       | enumerate: [<_MainThread(MainThread, started 140505133541120)>, <ExcThread(job_monitor, started 140504788350720)>]
2019-08-21 07:08:02,454 | WARNING  | job_monitor         | pilot.control.job                | check_job_monitor_waiting_time | no jobs in monitored_payloads queue (waited for 62 s)
2019-08-21 07:08:02,455 | DEBUG    | job_monitor         | pilot.control.job                | job_monitor               | [job] job monitor thread has finished
2019-08-21 07:08:02,536 | INFO     | MainThread          | pilot.workflow.generic           | run                       | end of generic workflow (traces error code: 0)
2019-08-21 07:08:02,537 | INFO     | MainThread          | root                             | wrap_up                   | traces error code: 0
2019-08-21 07:08:02,537 | INFO     | MainThread          | root                             | wrap_up                   | pilot has finished
2019-08-21 07:08:02 UTC [wrapper] ==== pilot stdout END ====
2019-08-21 07:08:02 UTC [wrapper] ==== wrapper stdout RESUME ====
2019-08-21 07:08:02 UTC [wrapper] Pilot exit status: 0
2019-08-21 07:08:02 UTC [wrapper] STATUSCODE: 0
2019-08-21 07:08:02 UTC [wrapper] apfmon messages muted
---- find pandaID.out ----
insgesamt 44
-rw-rw-r--.  1 320 320 11357 25. Jul 16:38 LICENSE
drwxrwxr-x. 14 320 320   216 19. Aug 05:07 pilot
-rwxrwxr-x.  1 320 320 20463 25. Jul 16:38 pilot.py
-rw-r--r--.  1 320 320     8  7. Aug 13:02 PILOTVERSION
-rw-rw-r--.  1 320 320  2251 25. Jul 16:38 README.md
-rw-rw-r--.  1 320 320   221 25. Jul 16:38 TODO.md

2019-08-21 07:08:03 UTC [wrapper] Test setup, not cleaning
2019-08-21 07:08:03 UTC [wrapper] ==== wrapper stdout END ====
2019-08-21 07:08:03 UTC [wrapper] ==== wrapper stderr END ====
2019-08-21 07:08:03 UTC [wrapper] wrapper wrapperexiting ec=0, duration=187325
2019-08-21 07:08:03 UTC [wrapper] apfmon messages muted
2019-08-21 09:08:05,082: ***************diag file************
2019-08-21 09:08:05,082: runtimeenvironments=APPS/HEP/ATLAS-SITE;
Processors=1
WallTime=187325.25s
KernelTime=3480.07s
UserTime=177092.69s
CPUUsage=96%
MaxResidentMemory=1942096kB
AverageResidentMemory=0kB
AverageTotalMemory=0kB
AverageUnsharedMemory=0kB
AverageUnsharedStack=0kB
AverageSharedMemory=0kB
PageSize=4096B
MajorPageFaults=2935489
MinorPageFaults=85225102
Swaps=0
ForcedSwitches=23866761
WaitSwitches=80524464
Inputs=702902792
Outputs=678448
SocketReceived=0
SocketSent=0
Signals=0

nodename=maeax@apu10r
exitcode=0
2019-08-21 09:08:05,095: ******************************WorkDir***********************
2019-08-21 09:08:05,095: insgesamt 291952
drwxrwx--x. 6 root root      4096 21. Aug 09:08 .
drwxrwx--x. 3 root root        33 21. Aug 06:23 ..
-rw-------. 1 root root   7440670 19. Aug 05:07 agis_ddmendpoints.json
-rw-------. 1 root root   4379057 19. Aug 05:07 agis_schedconf.cvmfs.json
drwx------. 2 root root         6 19. Aug 05:06 .alrb
drwxr-xr-x. 3 root root        17 19. Aug 05:05 APPS
-rw-------. 1 root root       533 19. Aug 05:06 .asetup
-rw-------. 1 root root       826 19. Aug 05:09 .asetup.save
-rw-r--r--. 1 root root         0 19. Aug 05:05 boinc_lockfile
-rw-r--r--. 1 root root      8192 21. Aug 09:07 boinc_mmap_file
-rw-r--r--. 1 root root       539 21. Aug 09:05 boinc_task_state.xml
-rw-------. 1 root root        58 21. Aug 06:24 .directory
-rw-r--r--. 1 root root 277446164 19. Aug 05:05 EVNT.18605758._000438.pool.root.1
-rw-------. 1 root root       503 21. Aug 09:08 gLQODmOdZJvnShfckohDCDFpABFKDmABFKDm3KjLDmABFKDmphqs7m.diag
-rw-------. 1 root root     80830 21. Aug 09:07 heartbeat.json
-rw-r--r--. 1 root root      5854 19. Aug 05:05 init_data.xml
-rw-r--r--. 1 root root    261620 19. Aug 05:05 input.tar.gz
-rw-r--r--. 1 root root       112 19. Aug 05:05 job.xml
-rw-------. 1 root root   8013723 21. Aug 09:08 log.18722326._014041.job.log.1
-rw-------. 1 root root    666100 21. Aug 09:06 log.18722326._014041.job.log.tgz.1
-rw-------. 1 root root       391 21. Aug 09:08 output.list
-rw-------. 1 4871 1028      2914 18. Aug 14:38 pandaJobData.out
drwxr-xr-x. 3  320  320       174  7. Aug 13:02 pilot2
-rw-r--r--. 1 root root    253018 18. Aug 14:29 pilot2.tar.gz
-rw-------. 1 root root      8733 21. Aug 09:08 pilotlog.txt
-rw-r--r--. 1 root root      4468 18. Aug 14:36 queuedata.json
-rw-r--r--. 1 root root       815 19. Aug 05:05 RTE.tar.gz
-rwxr-xr-x. 1 root root      8466 19. Aug 05:05 run_atlas
-rwx------. 1 4871 1028     12641 18. Aug 14:38 runpilot2-wrapper.sh
-rw-r--r--. 1 root root       692 21. Aug 09:08 runtime_log
-rw-r--r--. 1 root root      6643 21. Aug 09:08 runtime_log.err
drwxrwx--x. 2 root root       131 21. Aug 09:08 shared
-rw-r--r--. 1 root root      8659 19. Aug 05:05 start_atlas.sh
-rw-r--r--. 1 root root     17702 21. Aug 09:08 stderr.txt
-rw-r--r--. 1 root root       107 19. Aug 05:05 wrapper_26015_x86_64-pc-linux-gnu
-rw-r--r--. 1 root root        30 21. Aug 09:07 wrapper_checkpoint.txt

2019-08-21 09:08:05,095: running start_atlas return value is 0
2019-08-21 09:08:05,096: Parent exit 0
2019-08-21 09:08:05,096: child process exit 0
09:08:05 (3109): run_atlas exited; CPU time 177093.763902
09:08:05 (3109): called boinc_finish(0)

</stderr_txt>
]]>

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